REFERENCE

Acharya, M., Borland, G., Edkins, A. L., Maclellan, L. M., Matheson, J., Ozanne, B. W., & Cushley, W. (2010). CD23/FcepsilonRII: molecular multi-tasking. Clin Exp Immunol, 162 (1), 12-23. doi:10.1111/j.1365-2249.2010.04210.x
Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet, Chapter 7 , Unit7 20. doi:10.1002/0471142905.hg0720s76
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., . . . Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations.Nat Methods, 7 (4), 248-249. doi:10.1038/nmeth0410-248
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol, 215 (3), 403-410. doi:10.1016/S0022-2836(05)80360-2
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25 (17), 3389-3402.
Anoosha, P., Sakthivel, R., & Michael Gromiha, M. (2016). Exploring preferred amino acid mutations in cancer genes: Applications to identify potential drug targets. Biochim Biophys Acta, 1862 (2), 155-165. doi:10.1016/j.bbadis.2015.11.006
Asati, V., Mahapatra, D. K., & Bharti, S. K. (2016). PI3K/Akt/mTOR and Ras/Raf/MEK/ERK signaling pathways inhibitors as anticancer agents: Structural and pharmacological perspectives. Eur J Med Chem, 109 , 314-341. doi:10.1016/j.ejmech.2016.01.012
Beadling, C., Heinrich, M. C., Warrick, A., Forbes, E. M., Nelson, D., Justusson, E., . . . Corless, C. L. (2011). Multiplex mutation screening by mass spectrometry evaluation of 820 cases from a personalized cancer medicine registry. J Mol Diagn, 13 (5), 504-513. doi:10.1016/j.jmoldx.2011.04.003
Benetatos, L., Voulgaris, E., & Vartholomatos, G. (2017). The crosstalk between long non-coding RNAs and PI3K in cancer. Med Oncol, 34 (3), 39. doi:10.1007/s12032-017-0897-2
Bromberg, Y., & Rost, B. (2009). Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics, 10 Suppl 8 , S8. doi:10.1186/1471-2105-10-S8-S8
Care, M. A., Needham, C. J., Bulpitt, A. J., & Westhead, D. R. (2007). Deleterious SNP prediction: be mindful of your training data! Bioinformatics, 23 (6), 664-672. doi:10.1093/bioinformatics/btl649
Carter, H., Chen, S., Isik, L., Tyekucheva, S., Velculescu, V. E., Kinzler, K. W., . . . Karchin, R. (2009). Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res, 69 (16), 6660-6667. doi:10.1158/0008-5472.CAN-09-1133
Chang, C. C., & Lin, C. J. (2011). LIBSVM: A Library for Support Vector Machines. Acm Transactions on Intelligent Systems and Technology, 2 (3). doi:Artn 27
10.1145/1961189.1961199
Cheng, J., Randall, A. Z., Sweredoski, M. J., & Baldi, P. (2005). SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res, 33 (Web Server issue), W72-76. doi:10.1093/nar/gki396
Choi, Y., Sims, G. E., Murphy, S., Miller, J. R., & Chan, A. P. (2012). Predicting the functional effect of amino acid substitutions and indels. PLoS One, 7 (10), e46688. doi:10.1371/journal.pone.0046688
Chou, K. C. (2001). Prediction of protein cellular attributes using pseudo-amino acid composition.Proteins, 43 (3), 246-255.
David, A., Razali, R., Wass, M. N., & Sternberg, M. J. (2012). Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Hum Mutat, 33 (2), 359-363. doi:10.1002/humu.21656
Delespesse, G., Suter, U., Mossalayi, D., Bettler, B., Sarfati, M., Hofstetter, H., . . . Dalloul, A. (1991). Expression, structure, and function of the CD23 antigen. Adv Immunol, 49 , 149-191. doi:10.1016/s0065-2776(08)60776-2
Dhaliwal, B., Pang, M. O., Yuan, D., Yahya, N., Fabiane, S. M., McDonnell, J. M., . . . Sutton, B. J. (2013). Conformational plasticity at the IgE-binding site of the B-cell receptor CD23. Mol Immunol, 56 (4), 693-697. doi:10.1016/j.molimm.2013.07.005
Dong, P., Konno, Y., Watari, H., Hosaka, M., Noguchi, M., & Sakuragi, N. (2014). The impact of microRNA-mediated PI3K/AKT signaling on epithelial-mesenchymal transition and cancer stemness in endometrial cancer. J Transl Med, 12 , 231. doi:10.1186/s12967-014-0231-0
Ferrer-Costa, C., Gelpi, J. L., Zamakola, L., Parraga, I., de la Cruz, X., & Orozco, M. (2005). PMUT: a web-based tool for the annotation of pathological mutations on proteins.Bioinformatics, 21 (14), 3176-3178. doi:10.1093/bioinformatics/bti486
Fourcade, C., Arock, M., Ktorza, S., Ouaaz, F., Merle-Beral, H., Mentz, F., . . . Mossalayi, M. D. (1992). Expression of CD23 by human bone marrow stromal cells. Eur Cytokine Netw, 3 (6), 539-543.
Guo, W., Chen, Y., Zhou, X., Kar, A., Ray, P., Chen, X., . . . Wu, J. Y. (2011). An ALS-associated mutation affecting TDP-43 enhances protein aggregation, fibril formation and neurotoxicity. Nat Struct Mol Biol, 18 (7), 822-830. doi:10.1038/nsmb.2053
Halasi, M., Wang, M., Chavan, T. S., Gaponenko, V., Hay, N., & Gartel, A. L. (2013). ROS inhibitor N-acetyl-L-cysteine antagonizes the activity of proteasome inhibitors.Biochem J, 454 (2), 201-208. doi:10.1042/BJ20130282
Heffron, T. P., Heald, R. A., Ndubaku, C., Wei, B., Augistin, M., Do, S., . . . Olivero, A. G. (2016). The Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1 ,4]oxazepin-9-yl)oxy)propanamide (GDC-0326). J Med Chem, 59 (3), 985-1002. doi:10.1021/acs.jmedchem.5b01483
Hemmings, B. A., & Restuccia, D. F. (2012). PI3K-PKB/Akt pathway. Cold Spring Harb Perspect Biol, 4 (9), a011189. doi:10.1101/cshperspect.a011189
Henikoff, S., & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 89 (22), 10915-10919.
Hou, P., Liu, D., Shan, Y., Hu, S., Studeman, K., Condouris, S., . . . Xing, M. (2007). Genetic alterations and their relationship in the phosphatidylinositol 3-kinase/Akt pathway in thyroid cancer. Clin Cancer Res, 13 (4), 1161-1170. doi:10.1158/1078-0432.CCR-06-1125
Huang, Y., Niu, B., Gao, Y., Fu, L., & Li, W. (2010). CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26 (5), 680-682. doi:10.1093/bioinformatics/btq003
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci, 8 (3), 275-282.
Jones, S., Wang, T. L., Shih Ie, M., Mao, T. L., Nakayama, K., Roden, R., . . . Papadopoulos, N. (2010). Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science, 330 (6001), 228-231. doi:10.1126/science.1196333
Juritz, E., Fornasari, M. S., Martelli, P. L., Fariselli, P., Casadio, R., & Parisi, G. (2012). On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions. BMC Genomics, 13 Suppl 4 , S5. doi:10.1186/1471-2164-13-S4-S5
Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22 (12), 2577-2637. doi:10.1002/bip.360221211
Kaminker, J. S., Zhang, Y., Watanabe, C., & Zhang, Z. (2007). CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res, 35 (Web Server issue), W595-598. doi:10.1093/nar/gkm405
Kim, E., Tam, M., Siems, W. F., & Kang, C. (2005). Effects of drugs with muscle-related side effects and affinity for calsequestrin on the calcium regulatory function of sarcoplasmic reticulum microsomes. Mol Pharmacol, 68 (6), 1708-1715. doi:10.1124/mol.105.016253
Kinross, K. M., Montgomery, K. G., Kleinschmidt, M., Waring, P., Ivetac, I., Tikoo, A., . . . Phillips, W. A. (2012). An activating Pik3ca mutation coupled with Pten loss is sufficient to initiate ovarian tumorigenesis in mice. J Clin Invest, 122 (2), 553-557. doi:10.1172/JCI59309
Krauss, S., Mayer, E., Rank, G., & Rieber, E. P. (1993). Induction of the low affinity receptor for IgE (Fc epsilon RII/CD23) on human blood dendritic cells by interleukin-4.Adv Exp Med Biol, 329 , 231-236. doi:10.1007/978-1-4615-2930-9_39
Kuo, K. T., Mao, T. L., Jones, S., Veras, E., Ayhan, A., Wang, T. L., . . . Shih Ie, M. (2009). Frequent activating mutations of PIK3CA in ovarian clear cell carcinoma. Am J Pathol, 174 (5), 1597-1601. doi:10.2353/ajpath.2009.081000
Li, B., Krishnan, V. G., Mort, M. E., Xin, F., Kamati, K. K., Cooper, D. N., . . . Radivojac, P. (2009). Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics, 25 (21), 2744-2750. doi:10.1093/bioinformatics/btp528
Li, J., Su, Z., Ma, Z. Q., Slebos, R. J., Halvey, P., Tabb, D. L., . . . Zhang, B. (2011). A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics, 10 (5), M110 006536. doi:10.1074/mcp.M110.006536
Lin, C. P., Huang, S. W., Lai, Y. L., Yen, S. C., Shih, C. H., Lu, C. H., . . . Hwang, J. K. (2008). Deriving protein dynamical properties from weighted protein contact number.Proteins, 72 (3), 929-935. doi:10.1002/prot.21983
Lopez-Ferrando, V., Gazzo, A., de la Cruz, X., Orozco, M., & Gelpi, J. L. (2017). PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update.Nucleic Acids Res, 45 (W1), W222-W228. doi:10.1093/nar/gkx313
Lori, C., Lantella, A., Pasquo, A., Alexander, L. T., Knapp, S., Chiaraluce, R., & Consalvi, V. (2013). Effect of single amino acid substitution observed in cancer on Pim-1 kinase thermodynamic stability and structure. PLoS One, 8 (6), e64824. doi:10.1371/journal.pone.0064824
Lu, C. H., Chen, Y. C., Yu, C. S., & Hwang, J. K. (2007). Predicting disulfide connectivity patterns.Proteins, 67 (2), 262-270. doi:10.1002/prot.21309
Ma, Y. S., Huang, T., Zhong, X. M., Zhang, H. W., Cong, X. L., Xu, H., . . . Fu, D. (2018). Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis. Mol Cancer, 17 (1), 139. doi:10.1186/s12943-018-0890-1
MacLennan, D. H., Abu-Abed, M., & Kang, C. (2002). Structure-function relationships in Ca(2+) cycling proteins. J Mol Cell Cardiol, 34 (8), 897-918. doi:10.1006/jmcc.2002.2031
Manno, C., Figueroa, L. C., Gillespie, D., Fitts, R., Kang, C., Franzini-Armstrong, C., & Rios, E. (2017). Calsequestrin depolymerizes when calcium is depleted in the sarcoplasmic reticulum of working muscle. Proc Natl Acad Sci U S A, 114 (4), E638-E647. doi:10.1073/pnas.1620265114
McFarland, C. D., Yaglom, J. A., Wojtkowiak, J. W., Scott, J. G., Morse, D. L., Sherman, M. Y., & Mirny, L. A. (2017). The Damaging Effect of Passenger Mutations on Cancer Progression. Cancer Res, 77 (18), 4763-4772. doi:10.1158/0008-5472.CAN-15-3283-T
Nie, S., Yin, H., Tan, Z., Anderson, M. A., Ruffin, M. T., Simeone, D. M., & Lubman, D. M. (2014). Quantitative analysis of single amino acid variant peptides associated with pancreatic cancer in serum by an isobaric labeling quantitative method. J Proteome Res, 13 (12), 6058-6066. doi:10.1021/pr500934u
Niroula, A., & Vihinen, M. (2015). Harmful somatic amino acid substitutions affect key pathways in cancers.BMC Med Genomics, 8 , 53. doi:10.1186/s12920-015-0125-x
Parsons, D. W., Jones, S., Zhang, X., Lin, J. C., Leary, R. J., Angenendt, P., . . . Kinzler, K. W. (2008). An integrated genomic analysis of human glioblastoma multiforme.Science, 321 (5897), 1807-1812. doi:10.1126/science.1164382
Pita, J. M., Figueiredo, I. F., Moura, M. M., Leite, V., & Cavaco, B. M. (2014). Cell cycle deregulation and TP53 and RAS mutations are major events in poorly differentiated and undifferentiated thyroid carcinomas. J Clin Endocrinol Metab, 99 (3), E497-507. doi:10.1210/jc.2013-1512
Ponzoni, L., & Bahar, I. (2018). Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A, 115 (16), 4164-4169. doi:10.1073/pnas.1715896115
Radusky, L., Modenutti, C., Delgado, J., Bustamante, J. P., Vishnopolska, S., Kiel, C., . . . Turjanski, A. (2018). VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. Front Genet, 9 , 620. doi:10.3389/fgene.2018.00620
Redler, R. L., Das, J., Diaz, J. R., & Dokholyan, N. V. (2016). Protein Destabilization as a Common Factor in Diverse Inherited Disorders. J Mol Evol, 82 (1), 11-16. doi:10.1007/s00239-015-9717-5
Reeb, J., Hecht, M., Mahlich, Y., Bromberg, Y., & Rost, B. (2016). Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol, 12 (8), e1005047. doi:10.1371/journal.pcbi.1005047
Renaud, S., Seitlinger, J., Falcoz, P. E., Schaeffer, M., Voegeli, A. C., Legrain, M., . . . Massard, G. (2016). Specific KRAS amino acid substitutions and EGFR mutations predict site-specific recurrence and metastasis following non-small-cell lung cancer surgery. Br J Cancer, 115 (3), 346-353. doi:10.1038/bjc.2016.182
Rieber, E. P., Rank, G., Kohler, I., & Krauss, S. (1993). Membrane expression of Fc epsilon RII/CD23 and release of soluble CD23 by follicular dendritic cells. Adv Exp Med Biol, 329 , 393-398.
Sanchez, E. J., Lewis, K. M., Danna, B. R., & Kang, C. (2012). High-capacity Ca2+ binding of human skeletal calsequestrin. J Biol Chem, 287 (14), 11592-11601. doi:10.1074/jbc.M111.335075
Schaefer, C., & Rost, B. (2012). Predict impact of single amino acid change upon protein structure.BMC Genomics, 13 Suppl 4 , S4. doi:10.1186/1471-2164-13-S4-S4
Schrödinger, L. (2015). The PyMOL Molecular Graphics System, Version 1.8.
Shih, C. H., Chang, C. M., Lin, Y. S., Lo, W. C., & Hwang, J. K. (2012). Evolutionary information hidden in a single protein structure. Proteins, 80 (6), 1647-1657. doi:10.1002/prot.24058
Shihab, H. A., Gough, J., Cooper, D. N., Day, I. N., & Gaunt, T. R. (2013). Predicting the functional consequences of cancer-associated amino acid substitutions.Bioinformatics, 29 (12), 1504-1510. doi:10.1093/bioinformatics/btt182
Sim, N. L., Kumar, P., Hu, J., Henikoff, S., Schneider, G., & Ng, P. C. (2012). SIFT web server: predicting effects of amino acid substitutions on proteins.Nucleic Acids Res, 40 (Web Server issue), W452-457. doi:10.1093/nar/gks539
Son, H., Kang, H., Kim, H. S., & Kim, S. (2017). Somatic mutation driven codon transition bias in human cancer. Sci Rep, 7 (1), 14204. doi:10.1038/s41598-017-14543-1
Song, C., Wang, F., Cheng, K., Wei, X., Bian, Y., Wang, K., . . . Zou, H. (2014). Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. J Proteome Res, 13 (1), 241-248. doi:10.1021/pr400544j
Stewart, T. A., Yapa, K. T., & Monteith, G. R. (2015). Altered calcium signaling in cancer cells.Biochim Biophys Acta, 1848 (10 Pt B), 2502-2511. doi:10.1016/j.bbamem.2014.08.016
Stransky, N., Egloff, A. M., Tward, A. D., Kostic, A. D., Cibulskis, K., Sivachenko, A., . . . Grandis, J. R. (2011). The mutational landscape of head and neck squamous cell carcinoma. Science, 333 (6046), 1157-1160. doi:10.1126/science.1208130
Sundaram, L., Gao, H., Padigepati, S. R., McRae, J. F., Li, Y., Kosmicki, J. A., . . . Farh, K. K. (2018). Predicting the clinical impact of human mutation with deep neural networks. Nat Genet, 50 (8), 1161-1170. doi:10.1038/s41588-018-0167-z
Sunyaev, S., Ramensky, V., & Bork, P. (2000). Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet, 16 (5), 198-200.
Szpiech, Z. A., Strauli, N. B., White, K. A., Ruiz, D. G., Jacobson, M. P., Barber, D. L., & Hernandez, R. D. (2017). Prominent features of the amino acid mutation landscape in cancer. PLoS One, 12 (8), e0183273. doi:10.1371/journal.pone.0183273
Tan, H., Bao, J., & Zhou, X. (2015). Genome-wide mutational spectra analysis reveals significant cancer-specific heterogeneity. Sci Rep, 5 , 12566. doi:10.1038/srep12566
Teng, S., Srivastava, A. K., Schwartz, C. E., Alexov, E., & Wang, L. (2010). Structural assessment of the effects of amino acid substitutions on protein stability and protein protein interaction. Int J Comput Biol Drug Des, 3 (4), 334-349. doi:10.1504/IJCBDD.2010.038396
Terentyev, D., Viatchenko-Karpinski, S., Gyorke, I., Volpe, P., Williams, S. C., & Gyorke, S. (2003). Calsequestrin determines the functional size and stability of cardiac intracellular calcium stores: Mechanism for hereditary arrhythmia.Proc Natl Acad Sci U S A, 100 (20), 11759-11764. doi:10.1073/pnas.1932318100
Tsuber, V., Kadamov, Y., Brautigam, L., Berglund, U. W., & Helleday, T. (2017). Mutations in Cancer Cause Gain of Cysteine, Histidine, and Tryptophan at the Expense of a Net Loss of Arginine on the Proteome Level. Biomolecules, 7 (3). doi:10.3390/biom7030049
Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M., & Ng, P. C. (2016). SIFT missense predictions for genomes. Nat Protoc, 11 (1), 1-9. doi:10.1038/nprot.2015.123
Vercelli, D., Jabara, H. H., Lee, B. W., Woodland, N., Geha, R. S., & Leung, D. Y. (1988). Human recombinant interleukin 4 induces Fc epsilon R2/CD23 on normal human monocytes.J Exp Med, 167 (4), 1406-1416. doi:10.1084/jem.167.4.1406
Wang, B., Li, J., Cheng, X., Zhou, Q., Yang, J., Zhang, M., . . . Li, J. (2018). NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. Sci Rep, 8 (1), 6021. doi:10.1038/s41598-018-24286-2
Wang, X., Wei, X., Thijssen, B., Das, J., Lipkin, S. M., & Yu, H. (2012). Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol, 30 (2), 159-164. doi:10.1038/nbt.2106
Woischke, C., Schaaf, C. W., Yang, H. M., Vieth, M., Veits, L., Geddert, H., . . . Horst, D. (2017). In-depth mutational analyses of colorectal neuroendocrine carcinomas with adenoma or adenocarcinoma components. Mod Pathol, 30 (1), 95-103. doi:10.1038/modpathol.2016.150
Yates, C. M., Filippis, I., Kelley, L. A., & Sternberg, M. J. (2014). SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features.J Mol Biol, 426 (14), 2692-2701. doi:10.1016/j.jmb.2014.04.026
Yates, C. M., & Sternberg, M. J. (2013). Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs). J Mol Biol, 425 (8), 1274-1286. doi:10.1016/j.jmb.2013.01.026
Yu, C. S., Chen, Y. C., Lu, C. H., & Hwang, J. K. (2006). Prediction of protein subcellular localization.Proteins, 64 (3), 643-651. doi:10.1002/prot.21018
Yu, C. S., & Lu, C. H. (2011). Identification of antifreeze proteins and their functional residues by support vector machine and genetic algorithms based on n-peptide compositions. PLoS One, 6 (5), e20445. doi:10.1371/journal.pone.0020445
Yuan, D., Keeble, A. H., Hibbert, R. G., Fabiane, S., Gould, H. J., McDonnell, J. M., . . . Dhaliwal, B. (2013). Ca2+-dependent structural changes in the B-cell receptor CD23 increase its affinity for human immunoglobulin E. J Biol Chem, 288 (30), 21667-21677. doi:10.1074/jbc.M113.480657
Yue, P., Li, Z., & Moult, J. (2005). Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol, 353 (2), 459-473. doi:10.1016/j.jmb.2005.08.020
Zhang, M., Wang, B., Xu, J., Wang, X., Xie, L., Zhang, B., . . . Li, J. (2017). CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. J Proteome Res, 16 (2), 421-432. doi:10.1021/acs.jproteome.6b00505